error while running protein -ligand cal in gmx_MMPBSA.

[parul goyal]

 INPUT COMMAND :gmx_MMPBSA -O -i mmpbsa.in -cs md_0_1.tpr -ci index.ndx -cg 1 13 -ct md_0_1.xtc -lm ben.mol2 -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

WHILE RUNNING TRYPSIN-BENZENE (protein-ligand complex).

[INFO   ] Starting gmx_MMPBSA v1.5.6+25.g309d2fe
[INFO   ] Command-line
  gmx_MMPBSA -O -i mmpbsa.in -cs md_0_1.tpr -ci index.ndx -cg 1 13 -ct md_0_1.xtc -lm ben.mol2 -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

[INFO   ] Checking mmpbsa.in input file...
[INFO   ] Checking mmpbsa.in input file...Done.

[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /home/parul/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO   ] tleap found! Using /home/parul/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO   ] parmchk2 found! Using /home/parul/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO   ] sander found! Using /home/parul/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /usr/bin/gmx
[INFO   ] Checking external programs...Done.

[INFO   ] Building AMBER topologies from GROMACS files...
[INFO   ] Get PDB files from GROMACS structures files...
[INFO   ] Making gmx_MMPBSA index for complex...
[INFO   ] Normal Complex: Saving group 1_13 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO   ] Generating ligand parameters from ben.mol2 file...
[ERROR  ] MMPBSA_Error /home/parul/anaconda3/envs/gmxMMPBSA/bin/parmchk2 failed when querying ben.mol2.
           Check the gmx_MMPBSA.log file to report the problem.
  File "/home/parul/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/parul/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
    app.make_prmtops()
  File "/home/parul/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 545, in make_prmtops
    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
  File "/home/parul/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 116, in buildTopology
    self.gmx2pdb()
  File "/home/parul/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 276, in gmx2pdb
    GMXMMPBSA_ERROR('%s failed when querying %s' % (parmchk2, self.FILES.ligand_mol2))
  File "/home/parul/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 169, in __init__
    raise exc(msg + '\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error: /home/parul/anaconda3/envs/gmxMMPBSA/bin/parmchk2 failed when querying ben.mol2
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.

please help me out parmchk2 failed when querying ben.mol2, I did not get this error ,as ambertools are installed perfectly 

[marioe911116]

Please, try using the topology with the flag -cp topol.top

[marioe911116]

to sum up, as we solved this offline...

topology conversion has some functions that are case-sensitive... that being said, if there is a mismatch between the name of the molecules in the .top and .itp file (e.g. ligand appears as BEN in the .top file and as ben in the .itp file), the programs will end up in error...